@sjcrh/proteinpaint-client 2.205.0 → 2.206.1

package/dist/block.mds.geneboxplot-EN344GEP.js

@@ -1,823 +0,0 @@
-import {
-  ase_color,
-  init_config,
-  measure,
-  showsingleitem_table
-} from "./chunk-S5UN4VIQ.js";
-import {
-  appear2 as appear,
-  axisstyle,
-  disappear2 as disappear,
-  font,
-  make_table_2col,
-  newpane,
-  sayerror,
-  to_svg
-} from "./chunk-J7JDCNLU.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-N635HDJ4.js";
-import "./chunk-T46FA72N.js";
-import {
-  Menu
-} from "./chunk-ELJX3QIQ.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import {
-  dofetch2
-} from "./chunk-JYOIO5UY.js";
-import "./chunk-YN5NY3D3.js";
-import "./chunk-RN4BOWRH.js";
-import "./chunk-IK2BO37K.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-D6G64XPJ.js";
-import "./chunk-W5J3LTYS.js";
-import {
-  axisTop
-} from "./chunk-YLJOZP4P.js";
-import {
-  linear,
-  log
-} from "./chunk-HDTFYTEL.js";
-import "./chunk-FXQXCOII.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// src/block.mds.geneboxplot.js
-var label_cnvgain = "CNV gain";
-var label_cnvloss = "CNV loss";
-var label_sv = "SV";
-var label_ase = "Allele-specific expression";
-var label_outlier = "Outlier expression";
-async function init(p) {
-  if (!p.genome) return alert("cannot initiate plot: genome missing");
-  const plot = p;
-  plot.tip = new Menu({ padding: "0px" });
-  if (plot.file || plot.url) {
-    plot.gecfg = {};
-  } else {
-    if (!plot.dslabel) return alert("dslabel missing");
-    if (!plot.querykey) return alert("querykey missing");
-    const d = plot.genome.datasets[plot.dslabel];
-    if (!d) return alert("invalid dataset label: " + plot.dslabel);
-    plot.gecfg = d.queries[plot.querykey];
-    if (!plot.gecfg) return alert("invalid query key: " + plot.querykey);
-  }
-  init_config(plot.gecfg);
-  if (p.block && p.block.debugmode) {
-    window.plot = plot;
-  }
-  plot.errdiv = plot.holder.append("div").style("margin", "10px");
-  const buttonrow = plot.holder.append("div").style("margin", "10px");
-  plot.buttonrow = buttonrow;
-  mayaddgrouperselect(plot);
-  const configdiv = plot.holder.append("div").style("margin", "10px").style("border", "solid 1px #ededed").style("padding", "10px").style("display", "none");
-  plot.table_boxplotstats = plot.holder.append("table").style("margin", "10px").style("border-spacing", "4px").style("border-collapse", "separate");
-  buttonrow.append("button").text("Log10").on("click", (event) => {
-    plot.uselog = !plot.uselog;
-    event.target.innerHTML = plot.uselog ? "Linear" : "Log10";
-    plot.place();
-  });
-  if (plot.sample) {
-    plot.sample.shown = true;
-    buttonrow.append("button").text(plot.sample.name + " toggle").on("click", () => {
-      plot.sample.shown = !plot.sample.shown;
-      plot.sample.line.attr("stroke-opacity", plot.sample.shown ? 1 : 0);
-      plot.sample.svgtext.attr("fill-opacity", plot.sample.shown ? 1 : 0);
-    });
-  }
-  if (plot.svcnv) {
-    buttonrow.append("button").text("SV/CNV options").on("click", () => {
-      if (configdiv.style("display") == "none") appear(configdiv);
-      else disappear(configdiv);
-    });
-    plot.svcnv.useloss = true;
-    plot.svcnv.usegain = true;
-    plot.cnvconfig = {};
-    plot.svconfig = {};
-    {
-      const row = configdiv.append("div");
-      const id = Math.random().toString();
-      row.append("input").attr("type", "checkbox").property("checked", true).attr("id", id).on("change", (event) => {
-        plot.svcnv.usegain = event.target.checked;
-        plot.cnvconfig.div.style("display", plot.svcnv.usegain || plot.svcnv.useloss ? "block" : "none");
-        loadplot(plot);
-      });
-      row.append("label").attr("for", id).attr("class", "sja_clbtext").html(" Add boxplot for samples with copy number gain over " + plot.gene).style("color", plot.color.cnvgain);
-    }
-    {
-      const row = configdiv.append("div");
-      const id = Math.random().toString();
-      row.append("input").attr("type", "checkbox").property("checked", true).attr("id", id).on("change", (event) => {
-        plot.svcnv.useloss = event.target.checked;
-        plot.cnvconfig.div.style("display", plot.svcnv.usegain || plot.svcnv.useloss ? "block" : "none");
-        loadplot(plot);
-      });
-      row.append("label").attr("for", id).attr("class", "sja_clbtext").html(" Add boxplot for samples with copy number loss over " + plot.gene).style("color", plot.color.cnvloss);
-    }
-    {
-      const d = configdiv.append("div");
-      plot.cnvconfig.div = d;
-      const d2 = d.append("div").style("display", "inline-block").style("margin", "5px 10px 10px 30px").style("border", "solid 1px #ededed").style("padding", "10px");
-      {
-        const row = d2.append("div").style("margin-bottom", "15px");
-        row.append("span").html("CNV log2(ratio) cutoff ");
-        row.append("input").property("value", plot.svcnv.valueCutoff || 0).attr("type", "number").style("width", "50px").on("keyup", (event) => {
-          if (event.code != "Enter" && event.code != "NumpadEnter") return;
-          let v = Number.parseFloat(event.target.value);
-          if (!v || v < 0) {
-            v = 0;
-          }
-          if (v == 0) {
-            if (plot.svcnv.valueCutoff) {
-              plot.svcnv.valueCutoff = 0;
-              loadplot(plot);
-            } else {
-            }
-            return;
-          }
-          if (plot.svcnv.valueCutoff) {
-            if (plot.svcnv.valueCutoff == v) {
-            } else {
-              plot.svcnv.valueCutoff = v;
-              loadplot(plot);
-            }
-          } else {
-            plot.svcnv.valueCutoff = v;
-            loadplot(plot);
-          }
-        });
-        row.append("div").style("font-size", ".7em").style("color", "#858585").html("CNV with absolute log2(ratio) lower than cutoff will not be considered. Set to 0 to cancel.");
-      }
-      {
-        const row = d2.append("div");
-        row.append("span").html("CNV segment size limit&nbsp;");
-        row.append("input").property("value", plot.svcnv.bplengthUpperLimit || 0).attr("type", "number").style("width", "80px").on("keyup", (event) => {
-          if (event.code != "Enter" && event.code != "NumpadEnter") return;
-          let v = Number.parseInt(event.target.value);
-          if (!v || v < 0) {
-            v = 0;
-          }
-          if (v == 0) {
-            if (plot.svcnv.bplengthUpperLimit) {
-              plot.svcnv.bplengthUpperLimit = 0;
-              loadplot(plot);
-            } else {
-            }
-            return;
-          }
-          if (plot.svcnv.bplengthUpperLimit) {
-            if (plot.svcnv.bplengthUpperLimit == v) {
-            } else {
-              plot.svcnv.bplengthUpperLimit = v;
-              loadplot(plot);
-            }
-          } else {
-            plot.svcnv.bplengthUpperLimit = v;
-            loadplot(plot);
-          }
-        });
-        row.append("span").html("&nbsp;bp");
-        row.append("div").style("font-size", ".7em").style("color", "#858585").html("CNV segment longer than cutoff will not be considered. Set to 0 to cancel.");
-      }
-    }
-    {
-      const row = configdiv.append("div");
-      const id = Math.random().toString();
-      row.append("input").attr("type", "checkbox").property("checked", false).attr("id", id).on("change", (event) => {
-        plot.svcnv.usesv = event.target.checked;
-        plot.svconfig.div.style("display", plot.svcnv.usesv ? "block" : "none");
-        loadplot(plot);
-      });
-      row.append("label").attr("for", id).attr("class", "sja_clbtext").html("&nbsp;Add boxplot for samples with structural variation over " + plot.gene).style("color", plot.color.sv);
-    }
-    {
-      const d = configdiv.append("div").style("display", "none");
-      plot.svconfig.div = d;
-      const d2 = d.append("div").style("display", "inline-block").style("margin", "5px 10px 10px 30px").style("border", "solid 1px #ededed").style("padding", "10px");
-      {
-        const row = d2.append("div");
-        row.append("span").html("Include SV from flanking region of length:&nbsp;");
-        row.append("input").property("value", 0).attr("type", "number").style("width", "80px").on("keyup", (event) => {
-          if (event.code != "Enter" && event.code != "NumpadEnter") return;
-          let v = Number.parseInt(event.target.value);
-          if (!v || v < 0) {
-            v = 0;
-          }
-          if (v == 0) {
-            if (plot.svcnv.svflank) {
-              plot.svcnv.svflank = 0;
-              loadplot(plot);
-            } else {
-            }
-            return;
-          }
-          if (plot.svcnv.svflank) {
-            if (plot.svcnv.svflank == v) {
-            } else {
-              plot.svcnv.svflank = v;
-              loadplot(plot);
-            }
-          } else {
-            plot.svcnv.svflank = v;
-            loadplot(plot);
-          }
-        });
-        row.append("span").html("&nbsp;bp");
-        row.append("div").style("font-size", ".7em").style("color", "#858585").html("Set to 0 to cancel.");
-      }
-    }
-  }
-  plot.buttonholder_boxplot = buttonrow.append("span");
-  plot.buttonholder_sampleexpdata = buttonrow.append("span");
-  buttonrow.append("button").text("SVG").on("click", () => {
-    to_svg(plot.svg.node(), "Expression");
-  });
-  plot.svg = plot.holder.append("svg");
-  const axisg = plot.svg.append("g");
-  plot.g0 = plot.svg.append("g");
-  const axisheight = 50;
-  const lablspace = 10;
-  const axisw = 500;
-  const rowheight = 16;
-  const rowspace = 10;
-  const _rowspace = 2;
-  const axispad2 = 30;
-  const fontsize = 14;
-  const circleyshift = 2;
-  plot.place = () => {
-    plot.axislabel.attr("x", axisw / 2);
-    let labwidth = 0;
-    let rightwidth = 0;
-    const scale0 = (plot.uselog ? log() : linear()).domain([plot.data.min == 0 ? 1e-3 : plot.data.min, plot.data.max]).range([0, axisw]);
-    const scale = (v) => {
-      if (plot.uselog) {
-        if (v == 0) return 0;
-      }
-      return scale0(v);
-    };
-    axisstyle({
-      axis: axisg.transition().call(axisTop().scale(scale0)),
-      showline: 1
-    });
-    let y = rowspace;
-    if (plot.data.lst) {
-      labwidth = 20;
-      rightwidth = 20;
-      for (const d of plot.data.lst) {
-        d.circle.transition().attr("cx", scale(d.value)).attr("cy", y).attr("r", rowheight / 2);
-        y += circleyshift;
-      }
-    } else {
-      for (const g of plot.data.groups) {
-        g.g.attr("transform", "translate(0," + y + ")");
-        const _rowheight = rowheight * (g.boxplots.length > 1 ? 0.8 : 1);
-        let _y = 0;
-        for (const bp of g.boxplots) {
-          if (bp.label) {
-            bp.label.attr("font-size", _rowheight).attr("x", axisw + 5).attr("y", _y + _rowheight / 2).each(function() {
-              rightwidth = Math.max(rightwidth, this.getBBox().width);
-            });
-          }
-          if (bp.hline) {
-            const w1 = scale(bp.w1);
-            const w2 = scale(bp.w2);
-            const p25 = scale(bp.p25);
-            const p50 = scale(bp.p50);
-            const p75 = scale(bp.p75);
-            bp.hline.transition().attr("x1", w1).attr("x2", w2).attr("y1", _y + _rowheight / 2).attr("y2", _y + _rowheight / 2);
-            bp.linew1.transition().attr("x1", w1).attr("x2", w1).attr("y1", _y).attr("y2", _y + _rowheight);
-            bp.linew2.transition().attr("x1", w2).attr("x2", w2).attr("y1", _y).attr("y2", _y + _rowheight);
-            bp.box.transition().attr("x", p25).attr("y", _y).attr("width", p75 - p25).attr("height", _rowheight);
-            bp.linep50.transition().attr("x1", p50).attr("x2", p50).attr("y1", _y).attr("y2", _y + _rowheight);
-          }
-          for (const d of bp.out) {
-            d.circle.transition().attr("cx", scale(d.value)).attr("cy", _y + _rowheight / 2).attr("r", _rowheight / 3);
-          }
-          _y += _rowheight + _rowspace;
-        }
-        const h = (_rowheight + _rowspace) * g.boxplots.length - _rowspace;
-        g.label.attr("x", -lablspace).attr("y", h / 2).attr("font-size", fontsize).each(function() {
-          labwidth = Math.max(labwidth, this.getBBox().width);
-        });
-        if (g.bg)
-          g.bg.attr("y", -rowspace / 2).attr("width", axisw).attr("height", h + rowspace);
-        y += h + rowspace;
-      }
-    }
-    plot.g0.attr("transform", "translate(" + (labwidth + lablspace) + "," + axisheight + ")");
-    axisg.attr("transform", "translate(" + (labwidth + lablspace) + "," + axisheight + ")");
-    if (plot.sample) {
-      plot.sample.g.transition().attr("transform", "translate(" + scale(plot.sample.value) + "," + y + ")");
-      plot.sample.line.attr("y1", -y);
-    }
-    plot.svg.attr("width", labwidth + lablspace + axisw + axispad2 + rightwidth).attr("height", axisheight + y + 30);
-  };
-  try {
-    await loadplot(plot);
-  } catch (e) {
-    sayerror(plot.errdiv, "Error: " + (e.message || e));
-    if (e.stack) console.log(e.stack);
-  }
-}
-async function loadplot(plot) {
-  const arg = {
-    genome: plot.genome.name,
-    gene: plot.gene,
-    chr: plot.chr,
-    start: plot.start,
-    stop: plot.stop,
-    svcnv: plot.svcnv,
-    index_boxplotgroupers: plot.index_boxplotgroupers,
-    sampleset: plot.sampleset
-  };
-  if (plot.dslabel) {
-    arg.dslabel = plot.dslabel;
-    arg.querykey = plot.querykey;
-  } else {
-    arg.iscustom = 1;
-    arg.file = plot.file;
-    arg.url = plot.url;
-    arg.indexURL = plot.indexURL;
-  }
-  plot.g0.append("text").text("Loading ...").attr("font-size", 20).attr("text-anchor", "center").attr("dominant-baseline", "central").attr("x", plot.svg.attr("width") / 2).attr("y", plot.svg.attr("height") / 2);
-  const data = await dofetch2("mdsgeneboxplot", { method: "POST", body: JSON.stringify(arg) });
-  if (data.error) throw data.error;
-  plot.g0.selectAll("*").remove();
-  plot.axislabel = plot.g0.append("text").attr("font-size", 14).attr("font-family", font).attr("text-anchor", "middle").attr("y", -25).text(plot.gene + " " + plot.gecfg.datatype);
-  plot.data = data;
-  const color0 = "green";
-  if (data.lst) {
-    addbutton_showdata_fromlst(plot);
-    for (const d of data.lst) {
-      d.circle = plot.g0.append("circle").attr("fill", "white").attr("fill-opacity", 0).attr("stroke", color0).attr("stroke-opacity", 0.8).on("mouseover", (event) => {
-        plot.tip.clear().d.append("div").style("margin", "10px").html(d.sample + "<br>" + d.value);
-        plot.tip.show(event.clientX, event.clientY);
-      }).on("mouseout", () => plot.tip.hide());
-      if (plot.clicksample) {
-        d.circle.on("click", () => {
-          plot.clicksample(d, null, plot);
-        });
-      }
-    }
-  } else {
-    addbutton_boxplotstats(plot);
-    addbutton_showdata_newquery(plot);
-    for (const [i, g] of data.groups.entries()) {
-      g.g = plot.g0.append("g");
-      if (i % 2 == 0) {
-        g.bg = g.g.append("rect").attr("fill", "#f5f5f5");
-      }
-      g.label = g.g.append("text").attr("font-family", font).attr("text-anchor", "end").attr("dominant-baseline", "central").attr("class", "sja_clbtext").text(g.name).on("click", (event) => {
-        init2(Math.max(100, event.clientX - 100), Math.max(100, event.clientY - 100), plot, g);
-      });
-      if (g.attributes) {
-        g.label.on("mouseover", (event) => {
-          plot.tip.clear().show(event.clientX, event.clientY);
-          const d = plot.tip.d.append("div").style("margin", "10px");
-          for (const a of g.attributes) {
-            d.append("div").html(
-              a.kvalue + (a.fullvalue ? ' <span style="opacity:.5;font-size:.8em;">' + a.fullvalue + "</span>" : "")
-            );
-          }
-        }).on("mouseout", () => {
-          plot.tip.hide();
-        });
-      }
-      for (const bp of g.boxplots) {
-        let color;
-        if (bp.iscnvgain) {
-          color = plot.color.cnvgain;
-          bp.label = g.g.append("text").text("CNV gain (" + bp.samplecount + ")");
-        } else if (bp.iscnvloss) {
-          color = plot.color.cnvloss;
-          bp.label = g.g.append("text").text("CNV loss (" + bp.samplecount + ")");
-        } else if (bp.issv) {
-          color = "black";
-          bp.label = g.g.append("text").text("SV (" + bp.samplecount + ")");
-        } else {
-          color = color0;
-        }
-        if (bp.label) {
-          bp.label.attr("fill", color).attr("font-family", font).attr("dominant-baseline", "central");
-        }
-        if (bp.w1 != void 0) {
-          bp.hline = g.g.append("line").attr("stroke", color).attr("shape-rendering", "crispEdges");
-          bp.linew1 = g.g.append("line").attr("stroke", color).attr("shape-rendering", "crispEdges");
-          bp.linew2 = g.g.append("line").attr("stroke", color).attr("shape-rendering", "crispEdges");
-          bp.box = g.g.append("rect").attr("fill", "white").attr("stroke", color).attr("shape-rendering", "crispEdges");
-          bp.linep50 = g.g.append("line").attr("stroke", color).attr("shape-rendering", "crispEdges");
-        }
-        for (const d of bp.out) {
-          d.circle = g.g.append("circle").attr("stroke", color).attr("fill", "white").attr("fill-opacity", 0).on("mouseover", (event) => {
-            plot.tip.clear().d.append("div").style("margin", "10px").html(d.sample + "<br>" + d.value);
-            plot.tip.show(event.clientX, event.clientY);
-          }).on("mouseout", () => {
-            plot.tip.hide();
-          });
-          if (plot.clicksample) {
-            d.circle.on("click", () => {
-              plot.clicksample(d, g, plot);
-            });
-          }
-        }
-      }
-    }
-  }
-  if (plot.sample) {
-    plot.sample.g = plot.g0.append("g");
-    plot.sample.svgtext = plot.sample.g.append("text").text(plot.sample.name).attr("font-family", font).attr("font-size", 12).attr("text-anchor", "middle").attr("dominant-baseline", "hanging").attr("fill", "blue");
-    plot.sample.line = plot.sample.g.append("line").attr("shape-rendering", "crispEdges").attr("stroke", "blue");
-  }
-  plot.place();
-}
-function addbutton_boxplotstats(plot) {
-  plot.buttonholder_boxplot.selectAll("*").remove();
-  plot.buttonholder_boxplot.append("button").text("Boxplots").on("click", () => {
-    if (plot.table_boxplotstats.style("display") == "block") {
-      disappear(plot.table_boxplotstats);
-      return;
-    }
-    plot.table_boxplotstats.selectAll("*").remove();
-    const tr = plot.table_boxplotstats.append("tr");
-    tr.append("td").text("Group").style("font-size", ".8em").style("opacity", 0.5);
-    tr.append("td").text("1st quartile").style("font-size", ".8em").style("opacity", 0.5);
-    tr.append("td").text("Median").style("font-size", ".8em").style("opacity", 0.5);
-    tr.append("td").text("3rd quartile").style("font-size", ".8em").style("opacity", 0.5);
-    for (const [i, g] of plot.data.groups.entries()) {
-      const tr2 = plot.table_boxplotstats.append("tr").style("background", i % 2 ? "" : "#f1f1f1");
-      tr2.append("td").text(g.name);
-      const boxplot = g.boxplots ? g.boxplots[0] : null;
-      tr2.append("td").text(boxplot ? boxplot.p25 : "");
-      tr2.append("td").text(boxplot ? boxplot.p50 : "");
-      tr2.append("td").text(boxplot ? boxplot.p75 : "");
-    }
-    appear(plot.table_boxplotstats);
-  });
-}
-function addbutton_showdata_fromlst(plot) {
-  plot.buttonrow.append("button").text(plot.gecfg.datatype).on("click", () => {
-    const pane = newpane({ x: 100, y: 100 });
-    pane.header.text(plot.gene + " " + plot.gecfg.datatype);
-    const table = pane.body.append("table").style("border-spacing", "4px").style("border-collapse", "separate");
-    const tr = table.append("tr");
-    tr.append("td").text("Sample").style("font-size", ".8em").style("opacity", 0.5);
-    tr.append("td").text(plot.gecfg.datatype).style("font-size", ".8em").style("opacity", 0.5);
-    for (const i of plot.data.lst) {
-      const tr2 = table.append("tr");
-      tr2.append("td").text(i.sample);
-      tr2.append("td").text(i.value);
-    }
-  });
-}
-function addbutton_showdata_newquery(plot) {
-  plot.buttonholder_sampleexpdata.selectAll("*").remove();
-  plot.buttonholder_sampleexpdata.append("button").text(plot.gecfg.datatype).on("click", async () => {
-    const pane = newpane({ x: 100, y: 100 });
-    pane.header.text(plot.gene + " " + plot.gecfg.datatype);
-    const wait = pane.body.append("div").style("margin", "30px").text("Loading...");
-    const arg = {
-      genome: plot.genome.name,
-      gene: plot.gene,
-      chr: plot.chr,
-      start: plot.start,
-      stop: plot.stop,
-      getalllst: 1
-    };
-    if (plot.dslabel) {
-      arg.dslabel = plot.dslabel;
-      arg.querykey = plot.querykey;
-    } else {
-      arg.iscustom = 1;
-      arg.file = plot.file;
-      arg.url = plot.url;
-      arg.indexURL = plot.indexURL;
-    }
-    try {
-      const data = await dofetch2("mdsgeneboxplot", { method: "POST", body: JSON.stringify(arg) });
-      if (data.error) throw data.error;
-      wait.remove();
-      const table = pane.body.append("table").style("border-spacing", "4px").style("border-collapse", "separate");
-      const tr = table.append("tr");
-      tr.append("td").text("Sample").style("font-size", ".8em").style("opacity", 0.5);
-      tr.append("td").text(plot.gecfg.datatype).style("font-size", ".8em").style("opacity", 0.5);
-      for (const i of data.lst) {
-        const tr2 = table.append("tr");
-        tr2.append("td").text(i.sample);
-        tr2.append("td").text(i.value);
-      }
-    } catch (e) {
-      wait.text("Error: " + (e.message || e));
-      if (e.stack) console.log(e.stack);
-    }
-  });
-}
-function init2(x, y, plot, group) {
-  const pane = newpane({ x, y });
-  pane.header.text(plot.gene + " " + plot.gecfg.datatype + " in " + group.name);
-  const pp = {
-    _plot: plot,
-    holder: pane.body,
-    uselog: plot.uselog
-  };
-  if (group.attributes) {
-    pp.getgroup = group.attributes;
-  } else {
-    pp.getgroup = 1;
-    pp.getgroup_unannotated = 1;
-  }
-  pp.errdiv = pp.holder.append("div").style("margin", "10px");
-  const buttonrow = pp.holder.append("div").style("margin", "10px");
-  const configdiv = pp.holder.append("div").style("margin", "10px").style("border", "solid 1px #ededed").style("padding", "10px").style("display", "none");
-  buttonrow.append("button").text("Log10").on("click", (event) => {
-    pp.uselog = !pp.uselog;
-    event.target.innerHTML = pp.uselog ? "Linear" : "Log10";
-    pp.place();
-  });
-  buttonrow.append("button").text("Data").on("click", () => {
-    const pane2 = newpane({ x: 200, y: 200 });
-    pane2.header.text(pane.header.node().innerHTML);
-    const table = pane2.body.append("table").style("border-spacing", "2px").style("border-collapse", "separate");
-    const tr = table.append("tr");
-    tr.append("td").text("Sample").style("font-size", ".8em").style("opacity", 0.5);
-    tr.append("td").text(plot.gecfg.datatype).style("font-size", ".8em").style("opacity", 0.5);
-    for (const [i, d] of pp.data.lst.entries()) {
-      const tr2 = table.append("tr");
-      const td = tr2.append("td").text(d.sample);
-      if (plot.clicksample) {
-        td.attr("class", "sja_clbtext").on("click", () => {
-          plot.clicksample(d, group, plot);
-        });
-      }
-      tr2.append("td").text(d.value);
-    }
-  });
-  pp.svg = pp.holder.append("svg");
-  pp.g0 = pp.svg.append("g");
-  const axisg = pp.svg.append("g");
-  const axiswidth = 400;
-  const circleradius = 6;
-  const axisticksize = 6;
-  const axislabelfontsize = 14;
-  const axispad = 10;
-  const statuscolpad = 5;
-  const circleyshift = 2;
-  pp.place = () => {
-    for (const col of pp.statuscolumns) {
-      col.width = 20;
-      for (const d of pp.data.lst) {
-        if (!d.status2cell) continue;
-        const cell = d.status2cell.get(col.name);
-        if (!cell) continue;
-        if (cell.label) {
-          cell.label.attr("font-size", circleradius * 2 - 2).each(function() {
-            col.width = Math.max(col.width, this.getBBox().width + 2);
-          });
-        }
-      }
-    }
-    let samplenamewidth = 0;
-    for (const d of pp.data.lst) {
-      if (d.samplelabel) {
-        d.samplelabel.attr("font-size", circleradius * 2 - 1).attr("x", -statuscolpad).attr("y", circleradius).each(function() {
-          samplenamewidth = Math.max(samplenamewidth, this.getBBox().width);
-        });
-      }
-    }
-    let statuslabelheight = 0;
-    let statustotalwidth = 0;
-    for (const col of pp.statuscolumns) {
-      if (!col.g) {
-        col.g = pp.g0.append("g");
-        col.namelabel = col.g.append("text").attr("font-family", font).attr("dominant-baseline", "central").attr("transform", "rotate(-90)").text(col.name);
-      }
-      col.g.attr("transform", "translate(" + (statustotalwidth + col.width / 2) + ",0)");
-      col.namelabel.attr("font-size", Math.min(15, col.width)).each(function() {
-        statuslabelheight = Math.max(statuslabelheight, this.getBBox().width);
-      });
-      statustotalwidth += col.width + statuscolpad;
-    }
-    statustotalwidth += circleradius;
-    const topheight = Math.max(statuslabelheight, axisticksize + axislabelfontsize + 20);
-    pp.g0.attr("transform", "translate(" + (samplenamewidth + statuscolpad) + "," + topheight + ")");
-    pp.axislabel.attr("x", statustotalwidth + axiswidth / 2);
-    axisg.attr("transform", "translate(" + (samplenamewidth + statuscolpad + statustotalwidth) + "," + topheight + ")");
-    const scale0 = (pp.uselog ? log() : linear()).domain([pp.data.min == 0 ? 1e-3 : pp.data.min, pp.data.max]).range([0, axiswidth]);
-    const scale = (v) => {
-      if (pp.uselog) {
-        if (v == 0) return 0;
-      }
-      return scale0(v);
-    };
-    axisstyle({
-      axis: axisg.transition().call(
-        axisTop().scale(scale0).tickSize(axisticksize)
-      ),
-      showline: 1
-    });
-    let y2 = axispad;
-    for (const [idx, d] of pp.data.lst.entries()) {
-      d.rowg.attr("transform", "translate(0," + y2 + ")");
-      if (d.rowbg) {
-        d.rowbg.attr("width", statustotalwidth + axiswidth).attr("height", circleradius * 2);
-      }
-      d.circle.transition().attr("r", circleradius).attr("cx", statustotalwidth + scale(d.value)).attr("cy", circleradius);
-      if (d.samplelabel) {
-        if (idx > 0 && !pp.data.lst[idx - 1].samplelabel) {
-          y2 += circleradius * 2 - circleyshift;
-          d.rowg.attr("transform", "translate(0," + y2 + ")");
-        }
-        if (d.status2cell) {
-          let x2 = 0;
-          for (const col of pp.statuscolumns) {
-            const cell = d.status2cell.get(col.name);
-            if (cell) {
-              cell.g.attr("transform", "translate(" + (x2 + col.width / 2) + "," + circleradius + ")");
-              cell.rect.attr("x", -col.width / 2).attr("y", -circleradius).attr("width", col.width).attr("height", circleradius * 2);
-            }
-            x2 += col.width + statuscolpad;
-          }
-        }
-        y2 += circleradius * 2;
-      } else {
-        y2 += circleyshift;
-      }
-    }
-    pp.svg.attr("width", samplenamewidth + statuscolpad + statustotalwidth + axiswidth + circleradius).attr("height", topheight + axispad + y2 + circleradius * 2);
-  };
-  pp.makegraph = () => {
-    const _p = pp._plot;
-    pp.axislabel = pp.g0.append("text").attr("font-size", 14).attr("font-family", font).attr("text-anchor", "middle").attr("y", -25).text(_p.gene + " " + _p.gecfg.datatype);
-    for (const d of pp.data.lst) {
-      measure(d, _p.gecfg);
-    }
-    let hasgain = false, hasloss = false, hassv = false, hasase = false, hasoutlier = false;
-    for (const d of pp.data.lst) {
-      if (d.gain) hasgain = true;
-      if (d.loss) hasloss = true;
-      if (d.sv) hassv = true;
-      if (d.estat.ase_monoallelic || d.estat.ase_uncertain || d.estat.ase_biallelic) hasase = true;
-      if (d.estat.outlier || d.estat.outlier_asehigh) hasoutlier = true;
-    }
-    pp.statuscolumns = [];
-    if (hasgain) {
-      pp.statuscolumns.push({
-        name: label_cnvgain
-        //width:20,
-      });
-    }
-    if (hasloss) {
-      pp.statuscolumns.push({
-        name: label_cnvloss
-        //width:20,
-      });
-    }
-    if (hassv) {
-      pp.statuscolumns.push({
-        name: label_sv,
-        width: 20
-      });
-    }
-    if (hasase) {
-      pp.statuscolumns.push({
-        name: label_ase,
-        width: 20
-      });
-    }
-    if (hasoutlier) {
-      pp.statuscolumns.push({
-        name: label_outlier,
-        width: 20
-      });
-    }
-    for (const d of pp.data.lst) {
-      d.rowg = pp.g0.append("g");
-      if (d.gain || d.loss || d.sv || d.estat.ase_monoallelic || d.estat.ase_biallelic || d.estat.ase_uncertain) {
-        d.rowbg = d.rowg.append("rect").attr("class", "sja_bgbox");
-      }
-      d.circle = d.rowg.append("circle").attr("fill", "white").attr("fill-opacity", 0).attr("stroke", "#858585").on("mouseover", (event) => {
-        tooltip_pp(d, _p.tip.clear().d, pp);
-        _p.tip.show(event.clientX, event.clientY);
-      }).on("mouseout", () => {
-        _p.tip.hide();
-      });
-      if (_p.clicksample) {
-        d.circle.on("click", () => {
-          _p.clicksample(d, group, _p);
-        });
-      }
-      const status2cell = /* @__PURE__ */ new Map();
-      if (d.gain) {
-        const cell = { g: d.rowg.append("g") };
-        cell.rect = cell.g.append("rect").attr("fill", _p.color.cnvgain);
-        status2cell.set(label_cnvgain, cell);
-      }
-      if (d.loss) {
-        const cell = { g: d.rowg.append("g") };
-        cell.rect = cell.g.append("rect").attr("fill", _p.color.cnvloss);
-        status2cell.set(label_cnvloss, cell);
-      }
-      if (d.sv) {
-        const cell = { g: d.rowg.append("g") };
-        cell.rect = cell.g.append("rect").attr("fill", _p.color.sv);
-        status2cell.set(label_sv, cell);
-      }
-      if (d.estat.ase_monoallelic || d.estat.ase_biallelic || d.estat.ase_uncertain) {
-        const cell = { g: d.rowg.append("g") };
-        cell.rect = cell.g.append("rect").attr("fill", ase_color(d, _p.gecfg)), cell.label = cell.g.append("text").text(d.estat.ase_monoallelic ? "Mono" : d.estat.ase_biallelic ? "Bi" : "?").attr("font-family", font).attr("dominant-baseline", "central").attr("text-anchor", "middle").attr("fill", "white");
-        status2cell.set(label_ase, cell);
-      }
-      if (d.estat.outlier) {
-        const cell = { g: d.rowg.append("g") };
-        cell.rect = cell.g.append("rect").attr("fill", _p.gecfg.outlier.color_outlier);
-        status2cell.set(label_outlier, cell);
-      } else if (d.estat.outlier_asehigh) {
-        const cell = { g: d.rowg.append("g") };
-        cell.rect = cell.g.append("rect").attr("fill", _p.gecfg.outlier.color_outlier_asehigh);
-        status2cell.set(label_outlier, cell);
-      }
-      if (status2cell.size) {
-        d.status2cell = status2cell;
-        d.samplelabel = d.rowg.append("text").attr("font-family", font).attr("text-anchor", "end").attr("dominant-baseline", "central").text(d.sample);
-      }
-    }
-    pp.place();
-  };
-  loadplot2(pp);
-}
-async function loadplot2(pp) {
-  const _p = pp._plot;
-  const arg = {
-    genome: _p.genome.name,
-    gene: _p.gene,
-    chr: _p.chr,
-    start: _p.start,
-    stop: _p.stop,
-    getgroup: pp.getgroup,
-    getgroup_unannotated: pp.getgroup_unannotated,
-    svcnv: _p.svcnv,
-    sampleset: _p.sampleset
-  };
-  if (_p.dslabel) {
-    arg.dslabel = _p.dslabel;
-    arg.querykey = _p.querykey;
-  } else {
-    arg.iscustom = 1;
-    arg.file = _p.file;
-    arg.url = _p.url;
-    arg.indexURL = _p.indexURL;
-  }
-  pp.g0.append("text").text("Loading ...").attr("font-size", 20).attr("text-anchor", "center").attr("dominant-baseline", "central").attr("x", pp.svg.attr("width") / 2).attr("y", pp.svg.attr("height") / 2);
-  try {
-    const data = await dofetch2("mdsgeneboxplot", { method: "POST", body: JSON.stringify(arg) });
-    if (data.error) throw data.error;
-    pp.g0.selectAll("*").remove();
-    pp.data = data;
-    pp.makegraph();
-  } catch (e) {
-    sayerror(pp.errdiv, "Error: " + (e.message || e));
-    if (e.stack) console.log(e.stack);
-  }
-}
-function tooltip_pp(d, holder, pp) {
-  const lst = [{ k: "sample", v: d.sample }, { k: pp._plot.gecfg.datatype, v: d.value }];
-  if (d.gain || d.loss || d.sv) {
-    const l2 = [];
-    if (d.gain) {
-      l2.push(
-        '<span style="padding:0px 5px;color:white;background:' + pp._plot.color.cnvgain + '">Copy number gain</span>'
-      );
-    }
-    if (d.loss) {
-      l2.push(
-        '<span style="padding:0px 5px;color:white;background:' + pp._plot.color.cnvloss + '">Copy number loss</span>'
-      );
-    }
-    if (d.sv) {
-      l2.push('<span style="padding:0px 5px;color:white;background:' + pp._plot.color.sv + '">SV</span>');
-    }
-    lst.push({ k: "Overlap", v: l2.join(" ") });
-  }
-  const table = make_table_2col(holder, lst);
-  showsingleitem_table(d, pp._plot.gecfg, table);
-}
-function mayaddgrouperselect(plot) {
-  if (!plot.boxplotgroupers) return;
-  const select = plot.buttonrow.append("select").on("change", (event) => {
-    plot.index_boxplotgroupers = event.target.selectedIndex;
-    loadplot(plot);
-  });
-  for (const [idx, name] of plot.boxplotgroupers.entries()) {
-    select.append("option").text(name);
-  }
-}
-export {
-  init
-};
-//# sourceMappingURL=block.mds.geneboxplot-EN344GEP.js.map